not a hack #25
not a hack #25
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| """ | ||
| This module provides pass-through access to PyCogent's denoiser code. It's a | ||
| bit of a hack, but it allows us to remove the direct dependency on PyCogent by |
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| """ | ||
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| from cogent.parse.flowgram import ( |
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Doesn't this force this module to be GPL?
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That's a really good point, damn licenses.
On (May-14-14|13:43), Daniel McDonald wrote:
+#!/usr/bin/env python
+
+"""
+This module provides pass-through access to PyCogent's denoiser code. It's a
+bit of a hack, but it allows us to remove the direct dependency on PyCogent by
+centralizing the denoiser code with all of the other PyCogent code that is
+targeted either for complete re-write or removal pending benchmarks. The basic
+idea is that it's not worth porting this code anywhere now because it's days are
+numbered, but we still need to be able to access it for the time being.
+
+May The Biological Research (application controller) Obsolescence Kit (brokit)
+be as short-lived as its name is awesome.
+
+"""
+
+from cogent.parse.flowgram import (Doesn't this force this module to be GPL?
Reply to this email directly or view it on GitHub:
https://github.com/biocore/brokit/pull/25/files#r12660158
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sorry...
we need more WTFPL
On Wed, May 14, 2014 at 2:45 PM, Yoshiki Vázquez Baeza <
[email protected]> wrote:
In brokit/denoiser.py:
+#!/usr/bin/env python
+
+"""
+This module provides pass-through access to PyCogent's denoiser code. It's a
+bit of a hack, but it allows us to remove the direct dependency on PyCogent by
+centralizing the denoiser code with all of the other PyCogent code that is
+targeted either for complete re-write or removal pending benchmarks. The basic
+idea is that it's not worth porting this code anywhere now because it's days are
+numbered, but we still need to be able to access it for the time being.
+
+May The Biological Research (application controller) Obsolescence Kit (brokit)
+be as short-lived as its name is awesome.
+
+"""
+
+from cogent.parse.flowgram import (That's a really good point, damn licenses.
… <#145fc7b88fc7157d_>
On (May-14-14|13:43), Daniel McDonald wrote: > +#!/usr/bin/env python > ++""" > +This module provides pass-through access to PyCogent's denoiser
code. It's a > +bit of a hack, but it allows us to remove the direct
dependency on PyCogent by > +centralizing the denoiser code with all of the
other PyCogent code that is > +targeted either for complete re-write or
removal pending benchmarks. The basic > +idea is that it's not worth
porting this code anywhere now because it's days are > +numbered, but we
still need to be able to access it for the time being. > + > +May The
Biological Research (application controller) Obsolescence Kit (brokit) >
+be as short-lived as its name is awesome. > + > +""" > + > +from
cogent.parse.flowgram import ( Doesn't this force this module to be GPL?
--- Reply to this email directly or view it on GitHub:
https://github.com/biocore/brokit/pull/25/files#r12660158—
Reply to this email directly or view it on GitHubhttps://github.com//pull/25/files#r12660257
.
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We discussed that, but it's not the only cogent import... Not sure how to
handle it, but the whole plan is that everything in here will either go
away all together or be re-written. Open to suggestions on how to handle
the situation.
On Wed, May 14, 2014 at 1:43 PM, Daniel McDonald
[email protected]:
In brokit/denoiser.py:
+#!/usr/bin/env python
+
+"""
+This module provides pass-through access to PyCogent's denoiser code. It's a
+bit of a hack, but it allows us to remove the direct dependency on PyCogent by
+centralizing the denoiser code with all of the other PyCogent code that is
+targeted either for complete re-write or removal pending benchmarks. The basic
+idea is that it's not worth porting this code anywhere now because it's days are
+numbered, but we still need to be able to access it for the time being.
+
+May The Biological Research (application controller) Obsolescence Kit (brokit)
+be as short-lived as its name is awesome.
+
+"""
+
+from cogent.parse.flowgram import (Doesn't this force this module to be GPL?
Reply to this email directly or view it on GitHubhttps://github.com//pull/25/files#r12660158
.
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Not sure, because if QIIME imports from here then QIIME is still GPL.
This one might be a relatively straightforward copy/paste, the only nightmare is Sequence, but it appears to only be used once here. That being said, one relatively straightforward thing has all kinds of demons laying around, and is yet another thing on top of the things to do.
I dont know any other way around this, basically importing from cogent is something that I believe needs to be avoided, otherwise brokit is GPL unless I'm misunderstanding something.
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QIIME is still GPL too though, right? So maybe the answer is that we make brokit GPL for now, and the target for QIIME 2.0 is no brokit dependency, and BSD license?
This one might be a relatively straightforward copy/paste, the only nightmare is Sequence
There are are tons of PyCogent imports in brokit, so there really isn't a simple solution here.
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Fun, okay.
I think that makes sense to change brokit to GPL.
On Wed, May 14, 2014 at 2:55 PM, Greg Caporaso [email protected]:
In brokit/denoiser.py:
+#!/usr/bin/env python
+
+"""
+This module provides pass-through access to PyCogent's denoiser code. It's a
+bit of a hack, but it allows us to remove the direct dependency on PyCogent by
+centralizing the denoiser code with all of the other PyCogent code that is
+targeted either for complete re-write or removal pending benchmarks. The basic
+idea is that it's not worth porting this code anywhere now because it's days are
+numbered, but we still need to be able to access it for the time being.
+
+May The Biological Research (application controller) Obsolescence Kit (brokit)
+be as short-lived as its name is awesome.
+
+"""
+
+from cogent.parse.flowgram import (QIIME is still GPL too though, right? So maybe the answer is that we make
brokit GPL for now, and the target for QIIME 2.0 is no brokit dependency,
and BSD license?This one might be a relatively straightforward copy/paste, the only
nightmare is SequenceThere are are tons of PyCogent imports in brokit, so there really isn't a
simple solution here.—
Reply to this email directly or view it on GitHubhttps://github.com//pull/25/files#r12660866
.
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Yeah, I think it's a necessary evil (a common theme with brokit).
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New issue for this (#27) and on the QIIME issue here. |
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Thanks for catching this @wasade. |
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That should have said @wasade, license whisperer. |
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This is how I feel about GPL:
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hah On Wed, May 14, 2014 at 3:23 PM, Yoshiki Vázquez Baeza <
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